Acknowledgment
We thank LetPub (www.letpub.com) for its linguistic assistance and scientific consultation during the preparation of this manuscript.
Fig. 1. Circular maps of the mitochondrial genomes of four cordyceps species. Genes are represented by different colored blocks. Colored blocks outside each ring indicate that the genes are on the direct strand, while colored blocks within the ring indicate that the genes are located on the reverse strand.
Fig. 2. The abundances of protein-coding, intronic, intergenic, and RNA gene regions (rRNAs and tRNAs) of the entire mitochondrial genomes from four cordyceps species.
Fig. 3. Codon usage in the mitochondrial genomes of the four cordyceps species. Codon numbers are plotted on the y-axis for A, Ophiocordyceps xuefengensis; B, Ophiocordyceps sinensis; C, Cordyceps militaris; D, Cordyceps brongniartii.
Fig. 4. RSCU values for 14 PCGs and rps3 in the mitochondrial genomes of four cordyceps.
Fig. 5. Variation in the length and base composition of each of the 14 PCGs and rps3 among four cordyceps mitogenomes. A, PCG length variation; B, GC content across PCGs; C, AT skew; D, GC skew.
Fig. 6. Genetic analysis of 14 PCGs and rps3 across four cordyceps mitogenomes. K2P, the overall mean Kimura-2-Parameter distance; Ka, the mean number of nonsynonymous substitutions per nonsynonymous site; Ks, the mean number of synonymous substitutions per synonymous site.
Fig. 7. Gene order comparison among four cordyceps mitogenomes.
Fig. 8. Colinearity analysis of four cordyceps mitogenomes, generated with Mauve 2.4.0. Two homologous regions were detected across the four mitochondrial genomes overall.
Fig. 9. Molecular phylogeny of 20 fungal species based on Bayesian inference (BI) and Maximum likelihood (ML) analysis of 14 PCGs andrps3 genes. Support values are Bayesian posterior probabilities (before slash) and bootstrap (BS) values (after slash). Species and NCBI accession numbers for genomes used in the phylogenetic analyses are provided in Supplementary Table S10.
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